Vagary
by Vault08
Summary: Spoilers! Commander Shepard has destroyed all synthetics, sacrificed himself, and, although at a hefty cost, destroyed the reapers. Suddenly, things are turned upside down when the truth is revealed, and everything will suddenly end in a question mark.
1. The Sacrifice

This was it.

All that was running through Shepard's mind, he had come this far, and after everything he'd been through, this was finally it. The three choices the ghostly child had presented him with would all end in the destruction of the reapers. It was this close to being over...but there was one choice that remained.

Control? Like the Illusive Man? What would he do with the reapers, just send them back to dark space and never let them show themselves again? He didn't know, it overwhelmed his mind just to think about it. Look what happened when the Illusive Man tried to take control, would he end up like that? Control seemed too...wrong, controlling your enemy? He couldn't do it, it wasn't right, something didn't sit with him right in his gut when he considered it.

Slowly, he shifted his gaze to directly in front of him. The large beam of the crucible, glowing with the possibility of the final stage of evolution.

Synthesis. This seemed like the most reasonable option, combine synthetics and organics, but would that really end well? The final stage of evolution? He thought it seemed appealing, but it seemed too perfect. Shepard couldn't trust it, he knew deep down that ever since he'd found out about the reapers, he'd had only one goal. Destroy them. Stop them. Not control them or find a workaround.

End them.

And he was more than willing to pay the cost to end the reaper threat with his own life.

He slowly started down to the right, gun in hand, to destroy the reapers. He recalled memories of fighting Sovereign, and finally taking him down. The assault on the Collector base, losing close friends he'd lost so much. People, trust, friends, colonies, crewmates, even Anderson was dead now, the man who was with him and believed him from the start, it had all been taking a toll on Shepard for a very long time. Now, his life was going to end it all, it was going to act as the final note on a song of tragedy, except this note, while seeming bleak, would be slightly uplifted, higher, than all the others.

As he made his way towards the glass chamber housing all the wires, he raised his gun, firing, first just one shot, then firing several times into them as he continued walking towards it, each shot causing a spark. Slowly, in his mind, he saw a picture of Liara, he loved her, he loved her so much, and it broke his heart to be breaking every promise he made to her about coming back, and blue children, with every shot he fired, but he had to do it. The reapers had to be stopped. He only hoped whatever happened to her, she ended up happy.

Finally, as he reached the glass and fired a final shot, a huge explosion quickly followed, sending him crashing to the floor and scarring his flesh with burns as the flames consumed him, ending his life. Explosions rang out on the Citadel, the flames ate away at his skin, but he didn't cry out in pain or fear, he had known this day would come for a long time.

The ultimate sacrifice.

It was finally over.


	2. The Arcane World

"John!"

Shepard lurched up and fell to the ground, off of whatever he was on. Where was he? Was he alive? He scrambled to feel for something, everything was so dark, he couldn't even see. He felt something, like a table, which he used to help himself up, his breathing was heavy, sweat coated his body, and he was in a panic. He felt something sliding down the side of his face. Sweat, blood, or tears? He had no idea.

"Hey! What is this?" He shouted.

Suddenly, the lights kicked on in the room and he was blinded, causing him to backwards onto a mattress. He heard a door on the far side of the room open, and several people entering. He blinked as fast as he could, slowly regaining his vision.

Anderson was standing before him, wearing an alliance issue uniform. Two men wearing white uniforms, clearly of some administration, were behind him, one had a needle, the other a clipboard. And behind both of them was a man. Human. Shepard recognized him. Kaidan!

"Anderson? But...how? You, you got shot. The Illusive Man shot you!"

Anderson sighed, and turned to the two men in white. "Give us a minute, thanks. Alenko, it's time." He said.

The two men exited quickly. Kaidan and Anderson pulled up two chairs and sat down in front of Shepard, staring at him with odd expressions of concern, like he was a test subject, or crazy. What was going on? The last thing Shepard remembered was burning, fire, shooting a pod...it was all really blurry right now, but he could've sworn he died.

Shepard slowly noticed the room he was in was more similar to a cell. Everything was so...white. Slowly, he glanced down, and his eyes widened in shock as he realized he was clad in purely white clothes, like he was a...patient.

What the hell was this?

"Anderson, talk to me. What's going on? Are the reapers dead?" Shepard asked, desperate for some answers.

The room was silent for about a minute before Anderson shifted in his seat, he seemed somewhat uneasy, like everything was misplaced.

"Shepard...we've been over this twice before with no progress, so I need you to bear with me on this. Do you remember Eden Prime, Shepard?" He asked, calmly.

"Eden Prime.." Shepard repeated, letting it hang in the air for a moment. So much had happened there. "That's where we found Javik. A live Prothean, I'll never forget.."

Kaidan started to say something, but Anderson raised his hand.

"But most of all, that's where we first found out about the Reapers. We were supposed to stop Saren, and we failed. Alenko, you were there, remember? We found out about the reapers. The visions, I could never forget..."

Anderson nodded. "Okay, Shepard. Do you remember the beacon?"

Shepard nodded. "Of course. The pain, the suffering, the extinction of the Protheans, all done by the reapers."

Anderson shook his head. "Okay, Shepard. Bear with me now, this is going to come as quite a shock and you won't believe it, but think hard. The beacon has turned you insane, Shepard. Doctors say it made your brain activity go off the charts. We don't know what the hell was in that thing, but we think it was a decoy deployed by Saren to kill you. It didn't succeed, but it did a number on your mind. Since then, you've been a patient here. You've stayed up all night screaming about Saren, the collectors, and then reapers. You describe some people who don't exist. Others who do...but you've never met."

Shepard stares at Anderson with a blank expression on his face. Several minutes pass with complete silence, before Shepard shifts and speaks.

"Anderson, what have the reapers done to you? How did they bring you back? Tell me, damn it! Alenko, where's the crucible?" Shepard shouted, standing up, his voice elevating consistently.

Suddenly Anderson stands up, and shoves Shepard onto the bed, "I am, damn it! I am! Listen to yourself! Sentient machines who wipe out organics? A mystical god child who created them? An indoctrinated, changed group of Protheans called the Collectors working for them? It doesn't make any sense, Shepard! Come to your senses!"

Shepard's expression turns to one of horror as he slowly realizes Anderson believes everything he said. Could it be true? Everything past the beacon on Eden Prime was...not real? No, no no, he remembered everything. The pain, the suffering, the sacrifices his crew and himself made, there was not a chance in hell it wasn't real, only moments prior he was feeling his flesh becoming scarred as a result of the fire.

"No!" Shepard shouted at Anderson, shaking his head. "If it was all in my mind, then how do you explain it in the first place? There was Prothean data in it!"

"I just said! We thought it was Prothean, it wasn't, it was a decoy used by Saren, working with the geth allowed him to use advanced technology, Saren planted it there for someone, not necessarily you, to find and die, eliminate a threat, you're not dead, but by all accounts, I'd say he eliminated that threat." Anderson stated firmly, before sitting down.

Shepard sat in silence, dumbfounded. What the hell was this? Was it true? Had he just, imagined everything? Was it all existent only in his mind? Or were the reapers doing this?

"Shepard...?" A familiar voice came from the doorway. Shepard quickly stood up.

"Liara! Liara, what's going on?" He asked, staring at her, searching for some sort of answer. But her expression wasn't anything that could help.

"Former Commander Shepard, meet Liara T'Soni." Kaidan said.

Liara gave a half smile, though her face was void of any sense of happiness or hope. "Hello again, John. I'm hoping this time we'll make some permanent progress with you, we've been watching you for a long time, trying to help you..." She said, her voice was low and calm, and it reminded Shepard of when he first met her.

"Liara, do you remember anything? Therum? Ilos? The Shadow Broker's base? Anything?" He said, placing a hand on her shoulder, desperate for some sort of evidence he wasn't crazy, his eyes were desperate, he was begging to hear something he thought was true.

"No, com-former commander, I am afraid I do not. I was researching a Prothean dig site years ago, but nothing ever came of it. I published it on my extranet blog, perhaps that's where you saw it...?" She asked, her eyes flickering with confusion and unknowing.

Shepard slowly sunk to the ground, sitting there, shaking his head. Liara slowly moved to sit down in another free chair. Hesitatingly, she inched forward to him.

"Shep-John. John, we're all here to help you, we just need you to see the truth." She said, shooting her glance to Kaidan and Anderson, not sure what to do.

"What happened to Saren?" Shepard asked, followed by a sigh.

"He escaped Eden Prime. Mr. Kaidan Alenko here was made the first human spectre and chased Saren all over the galaxy, it was a long, and tedious fight. Turned out Saren was breeding an army of-"

"Krogan on Virmire. And let me guess, Kaidan blew the place up, but left Ashley Williams to die in the blast?" Shepard asked.

Kaidan hesitated. "Halfway there. We blew the facility up, yes. Ashley Williams, though, no. We rescued her from Eden Prime, she continued to serve in the Alliance but after a few months called it quits. We kept in light contact...she, uh, committed suicide a little after she quit." Kaidan said, his words unsettled and distraught, it was evidently a touchy subject for him.

"What about Urdnot Wrex? Garrus Vakarian? Mordin Solus? Where are my crew?" Shepard said, elevating his voice, looking to anyone for an answer.

"Urdnot...Wrex?" Kaidan said, tilting his head. "Urdnot Wrex doesn't exist, we couldn't find any records of him. We came to the conclusion you made him up, sort of the pinnacle of the Krogan. Garrus helped me in my investigation into Saren, but I never saw him after that. Word is he was spotted on Omega, but that's it. And Mordin Solus? I don't know..."

"The salarian doctor. Word is, after years of torn feelings and guilt, he cured the genophage. Just a rumor for now, though." Liara added.

Shepard slowly brought his knees up to him and wrapped his arms around them. "How did you stop Saren?"

Kaidan spoke up, "He and his army of geth invaded the Citadel after Virmire, it was a long, hard battle, but I managed to take him down. Unfortunately, one of the geth ships blew up the Normandy, Joker and Chakwas and everyone but Garrus was killed. It was hard to see..." Kaidan said, slowly tuning away.

Shepard slowly shook his head, glancing up at Liara. "How could this have happened?"

Liara nodded, and gave a small sigh. "Well, whatever was in that decoy was destroyed after you used it, but from what we can tell, it was meant to kill you, but you survived. It sent your brain activity off the charts, and you gained a permanent, less common and more restrictive form of amnesia, you can remember everything up to Eden Prime fine. But after, it's a mess, you've managed to create your own alternate universe with these things, reading the news and what's going on with the universe influences this completely, and you find ways to work you and this crew you have into them, and from our studies, you're often confronted with harsh, almost unbearably tough decisions in this universe, where your actions ripple through the galaxy, but ultimately end up irrelevant in the end, because, as you've stated to us, you knew one way or the other you'd have to sacrifice yourself in the end. You often had to face unrealistic enemies, such as the collectors, which are just a myth, or the reapers, giant machines with lasers who destroy the galaxy." Liara said, recalling everything Shepard told her over the course of the last few years.

"What about the Illusive Man? Cerberus? I remember dying...the Normandy was destroyed. They...rebuilt me. Everyone escaped." Sheprd said, recalling the tragic events that had happened only 6 months prior.

"As Kaidan said, the Normandy was destroyed. You read about this, and eventually worked it into your universe. Everyone escaped except you, and you were rebuilt. You had to keep your universe going, so your mind merged the news into this alternate world and shaped you into it to be the leader." Liara explained, trying to sound as firmly as she could.

"Why don't I remember telling you all this?" Shepard asked, "You said I told you all this, how? When? I would've at least remembered a fragment of telling you this!"

"You were living in this alternate universe, you were having conversations with people who either don't exist, or do, but you've never seen or met them before. Myself or other doctors, occasionally Alliance Military, would listen in, gather what we could, and figure out this world you were living in. Sometimes, if we asked questions, you'd respond. Most of the time, you'd sit there, awake, talking to someone who wasn't there." She said, shaking her head. "We tried. Twice before, we've tried this exact thing, bringing you out of your "world" using extensive technology and psychological work, it failed the two times before, this is the last chance we get..." She said, turning away.

Shepard released his legs, smirking. "Or what?"

"Or...they're going to perform a surgery on you you probably won't survive." Anderson said, shaking his head.

Shepard slowly got up, looking at Liara, shaking his head, but the memories with her, aboard the Normandy, started coming back...suddenly, he leaned in to kiss her. She was taken aback, and moved away. Slowly, he looked at her.

"I'm sorry...John. I, I don't think that's appropriate..." She said, wiping her mouth.

Slowly, a tear ran down his face. Was all this true? Was it just some mind sequence he had? How was it possible? Well, it was unlikely he'd understand, but maybe it was true...

Suddenly, glancing out a window, Shepard saw a ghostly image of Harbinger, staring right at him.

"Commander Shepard. You failed. Our creator told you you could destroy all synthetics. What they did not tell you, was that you would rewrite history. The geth were destroyed with Saren, and now, nothing above a VI intelligence exists. You have doomed yourself. You do not know what reality is, Shepard. Your mental stability is gone. The Reapers will return in 50,000 years. Make peace, Commander Shepard. You will not see us again."

Slowly, Harbinger ascended into the sky. Shepard ran to the window and leaped into it, hitting the glass extremely hard, screaming at it.

"Harbinger! You son of a bitch! No! I stopped you! I stopped you! I did not fail! I did what I had to! You can't do this to me! No!" He screamed in agony, banging on the glass, trying to reach the other side in rage.

The two men dressed in white rush into the room and grab Shepard, and pin him to the ground. Slowly, he's injected with a large dose of sedative. Liara shakes her head, sighing. Anderson glances at Kaidan. Shepard slowly reaches up a hand towards Liara, who slowly backs away, cautious.

"Will he..." Liara started. One of the men turn, and nod.

"He will return to his alternate universe, keeping him out of it, after that, would likely kill him."

They slowly pick up his body and lay him back on the bed, shaking their heads.

"I thought we almost had him, sir." Kaidan said, shaking his head. "But I guess it's just too strong."

"Yeah.." Anderson replied. "I guess we just can't save him. I'm not giving up yet though, I'll try to postpone the surgery."

Liara slowly glanced out the window, seeing a figure of clouds resembling some sort of giant squid headed into the sky. "I wonder what he saw out there..." She asked herself under her breath, shaking her head.


	3. The Revival

London is in ruins. Nobody reached the beam, Hammer was completely annihilated. Rubble and fallen chunks of concrete litter the area surrounding the beam, which is still active. Harbinger is long gone, and Shepard could've sworn he just sacrificed himself, paying the ultimate price to rid the galaxy of the reapers once and for all, and secure peace...

There was a distant flicker of light. Voices. People. Doctors, maybe. He could hardly remember. It was all a blur to him.

Slowly, he felt himself come to. He couldn't explain how, but he knew he was alive. Quickly, he took a sharp breath, and opened his eyes.

He was alive.


End file.
